So this isn't a berger based PG rather a pure GROMOS one. But yes, it
also has problems. The double bond dihedrals don't work well and so you
get really poor order parameters after the double bond (see
http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is
true of POPG). From what I remember, this itp also has extraneous
dihedrals in the glycerol regions plus some other issues with the bonded
parameters (http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I
cannot remember off the top of my head the impact they made.
Up to you to decide with the density calculation.
Cheers
Tom
On 10/03/17 00:45, Merril Mathew wrote:
The POPG .itp and .pdb files were obtained from,
https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
Author : A Kukol.
I used D-POPG. Should I use electron density or mass for calculating
monolayer thickness?
Merril.
On 10 Mar 2017 00:36, "Thomas Piggot" <t.pig...@soton.ac.uk> wrote:
How did you get/make the itp for POPG, this isn't available from the
Tieleman group website. The Berger parameters don't work well for PG. For
example, you will see ring like structures in the head group if you look at
the simulations in something like VMD. The APL for bilayers (and I imagine
monolayers) will also be too low. You can find more details in
http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore models
are Berger based ones).
For the APL, the calculation is trivial using the box vectors (from gmx
energy or gmx traj). For the thickness, you can probably use gmx density to
create a density profile of your monolayer and work out a thickness from
that.
Tom
On 10/03/17 00:24, Merril Mathew wrote:
I am using Berger lipid from Dr.Tielemens website and modified the gromos
forcefield to include the lipid parameters. Out of interest, Do you know
any gromacs tools or other programs that calculatg the area per lipid and
bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
but
it only works with bilyer lipids. thanks.
Merril.
On 10 Mar 2017 00:19, "Thomas Piggot" <t.pig...@soton.ac.uk> wrote:
Sort of. The saturated carbons after the double bond will be correct too,
just not C9 and C10 in the double bond (as you need different assumptions
for calculating these in united-atom system which the -unsat option is
meant to do correctly but doesn't). Additionally, there are tools out
there
that will work for calculating the order parameters of the unsaturated
bond
if you need it.
GROMOS 53A6 is not really a lipid force field per say but there are PG
compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
lipid parameters are you using? Lots of them don't work well at all.
Cheers
Tom
On 10/03/17 00:10, Merril Mathew wrote:
Hi,
I am using a united atom forcefield. gromos53a6. So does that mean as
long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct? I understand it does not
describe
the full lipid length but can be used to assess the monolayer behaviour
roughly.
Merril.
On 10 Mar 2017 12:04 a.m., "Thomas Piggot" <t.pig...@soton.ac.uk>
wrote:
The order parameters calculated for all the saturated carbons will be
correct but the gmx order program doesn't calculate the order
parameters
for the unsaturated carbons correctly (even when using the -unsat
option).
Out of interest, is this a united-atom or all-atom force field you are
using?
Cheers
Tom
On 09/03/17 23:51, Merril Mathew wrote:
Hi,
I followed turorials found on Bevanlab by Justin. I successfully
calculated
order parameter for DPPC molecules in my system following the
tutorial.
My
question is whether the same calculation can be applied for a POPG
molecule
with a double bond in the acyl chain.? can I group all the carbon upto
the
double bond, therefore ignoring the double bond and the rest of the
carbons
in the chain to calculate order parameter? Is that a reasonable
analysis
to
measure the order of POPG molecules.? Thanks.
--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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University of Southampton, UK.
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Visiting Fellow
University of Southampton, UK.
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